,Unigene sequences were annotated by BlastX alignment to the non-redundant protein database (National Center for Biotechnology Information/GenBank) and the Aedes aegypti and Culex quinquefasciatus gene annotations (Vectorbase). This was done with a 1e-05 expectation value. Top hits are shown including accession numbers and description, if available. Unigene number and corresponding GenBank accession numbers are provided for all C. sonorensis genes. Both tables are modified from supplementary information tables at http://dx.doi.org/10.1371/journal.pone.0098123.s003 and numbered accordingly.,

We compared pollinator diversity derived from environmental DNA (eDNA) extracted from flowers and DNA extracted from pulverized bulk samples of insects collected from vane traps deployed at the same sites. We used three metabarcoding primers, two of which target arthropods generally (COI-Jusino and 16S-Marquina) and one that targets bumblebees (Bombus spp., COI-Milam). Across methods, we detected 77 insect families from 9 orders. The COI-Jusino marker amplified the highest taxonomic diversity compared to 16S-Marquina and COI-Milam. More ASVs were recovered from vane traps (blue: 1357, yellow: 1542) than flowers (245), but only 23% of families and 13% of genera were shared among methods, indicating that flowers and blue and yellow vane traps may each sample different parts of the available arthropod community. Of 29 flowers with known bee visitations, only 10 had bee detections, and incomplete reference databases hindered assignment to species.

,The small hive beetle (Aethina tumida, ATUMI) is an invasive parasite of bee colonies. ATUMI feeds on both fruits and bee nest products, facilitating its spread and increasing its impact on honey bees and other pollinators. The ATUMI genome has been sequenced and annotated, providing the first genomic resources for this species and for the Nitidulidae, a beetle family that is closely related to the extraordinarily species-rich clade of beetles known as the Phytophaga. ATUMI thus provides a contrasting view as a neighbor for one of the most successful known animal groups. A robust genome assembly and a gene set possessing 97.5% of the core proteins known from the holometabolous insects are presented. The ATUMI genome encodes fewer enzymes for plant digestion than the genomes of wood-feeding beetles, but nonetheless shows signs of broad metabolic plasticity. Gustatory receptors are few in number compared to other beetles, especially receptors with known sensitivity (in other beetles) to bitter substances. In contrast, several gene families implicated in detoxification of insecticides and adaptation to diverse dietary resources show increased copy numbers. The presence and diversity of homologs involved in detoxification differs substantially from the bee hosts of ATUMI. Results provide new insights into the genomic basis for local adaption and invasiveness in ATUMI, and a blueprint for control strategies that target this pest without harming their honey bee hosts. A minimal set of gustatory receptors is consistent with the observation that, once a host colony is invaded, food resources are predictable. Unique detoxification pathways and pathway members can help identify which treatments might control this species even in the presence of honey bees, which are notoriously sensitive to pesticides.,,

,The stable fly, Stomoxys calcitrans L. (Diptera: Muscidae), is one of the most significant pests of livestock in the United States. The identification of targets for the development of novel control for this pest species, focusing on those molecules that play a role in successful feeding and reproduction, is critical to mitigating its impact on confined and rangeland livestock. This data set was obtained from pyrosequencing of stable fly immature and adult specimens, comprising genes expressed at these stages. Stable fly specimens were obtained from an in vitro colony that is maintained at the Knipling-Bushland U.S. Livestock Insects Research Laboratory (Kerrville, TX) at 27°C, 60% RH, and a photoperiod of 12:12 [L:D] h. The stages included 1 g each of newly laid (t0) and 24 h post-oviposition (t24) embryos, 5 g of pooled 2nd–3rd instar larvae (late larvae), 2.5 g newly pupariated pupae (early pupae), 5 g pharate adults (pupae 2 d prior to eclosion; late pupae), and 1.5 g each of heads from unfed adult females and males (adult). Total RNA was isolated from various stages using the ToTALLY RNA Isolation Kit (Ambion, Foster City, CA) following the manufacturer’s protocol. Five micrograms of normalized cDNA was prepared for sequencing on the 454/ Roche GS-FLX. Double-stranded cDNA was nebulized to generate nominal 500-kb fragments and a shotgun library prepared for GS-FLX sequencing as per the manufacturer’s instructions (Roche, Indianapolis, IN). The sequencing library was run on a full picotitre plate and resulting data submitted to NCBI Short Read Archive (SRX018014). The resulting sequence data was assembled using newbler (RocheN) and the assembly optimized using a beta version of NGEN (DNAstar, Madison, WI) and Seqman (DNAstar, Oxford, UK). BLASTx was utilized based upon W.ND-BLAST (Dowd et al., 2005) against an embl-derived database for Drosophila (2008). Functional annotations were derived using DAVID (Dennis et al., 2003).,Raw reads were submitted to the Sequence Read Archive (SRA) Database at NCBI.,

,Supplemental information from a project describing the transcriptome of a beetle parasite of honey bees,The small hive beetle (SHB), Aethina tumida, is a major pest of managed honey bee (Apis mellifera) colonies in the United States and Australia, and an emergent threat in Europe. While strong honey bee colonies generally keep SHB populations in check, weak or stressed colonies can succumb to infestations. This parasite has spread from a sub-Saharan Africa to three continents, leading to immense management and regulatory costs. We performed a transcriptomic analysis involving deep sequencing of multiple life stages and both sexes of this species. The assembled transcriptome appears to be nearly complete, as judged by conserved insect orthologs and the ability to find plausible homologs for 11,952 proteins described from the genome of the red flour beetle. Expressed genes include each of the major metabolic, developmental and sensory groups, along with genes for proteins involved with immune defenses and insecticide resistance. We also present a total of 23,085 high-quality SNP's for the assembled contigs. We highlight potential differences between this beetle and its honey bee hosts, and suggest mechanisms of future research into the biology and control of this species. SNP resources will allow functional genetic analyses and analyses of dispersal for this invasive pest.,,

,Deep sequencing technologies were used to construct the first adult female Culicoides sonorensis reference transcriptome.,Genetic and genomic tools for Culicoides biting midges are lacking, despite the fact that they vector a large number of arboviruses and other pathogens impacting humans and domestic animals world-wide. Libraries of tissue-specific transcripts expressed in response to feeding and oral virus challenge in C. sonorensis have previously been reported, but extensive genome-wide expression profiling in the midge has not. Here, we successfully used deep sequencing technologies to construct the first adult female C. sonorensis reference transcriptome, and utilized genome-wide expression profiling to elucidate the genetic response to blood and sucrose feeding over time. The adult female midge unigene consists of 19,041 genes, of which less than 7% are differentially expressed during the course of a sucrose meal, while up to 52% of the genes respond significantly in blood-fed midges, indicating hematophagy induces complex physiological processes. Many genes that were differentially expressed during blood feeding were associated with digestion (e.g. proteases, lipases), hematophagy (e.g., salivary proteins), and vitellogenesis, revealing many major metabolic and biological factors underlying these critical processes. Additionally, key genes in the vitellogenesis pathway were identified, which provides the first glimpse into the molecular basis of anautogeny for C. sonorensis. This is the first extensive transcriptome for this genus, which will serve as a framework for future expression studies and in informing a reference genome assembly and annotation. Moreover, this study will serve as a foundation for subsequent studies of genome-wide expression analyses during early virus infection and dissecting the molecular mechanisms behind vector competence in midges.,

,To provide a foundation for identification of genomic loci for insecticide resistance and for discovery of new control technology, we report the sequencing, assembly, and annotation of the horn fly genome.,,

,The horn fly, Haematobia irritans irritans (Linnaeus, 1758; Diptera: Muscidae), a hematophagous external parasite of cattle, causes considerable economic losses to the livestock industry worldwide. This pest is mainly controlled with insecticides; however, horn fly populations from several countries have developed resistance to many of the products available for their control. In an attempt to better understand the adult horn fly and the development of resistance in natural populations, we used an Illumina paired-end read HiSeq and GAII approach to determine the transcriptomes of untreated control adult females, untreated control adult males, permethrin-treated surviving adult males and permethrin + piperonyl butoxide-treated killed adult males from a Louisiana population of horn flies with a moderate level of pyrethroid resistance. A total of 128,769,829, 127,276,458, 67,653,920, and 64,270,124 quality-filtered Illumina reads were obtained for untreated control adult females, untreated control adult males, permethrin-treated surviving adult males and permethrin + piperonyl butoxide-treated killed adult males, respectively. The de novo assemblies using CLC Genomics Workbench 8.0.1 yielded 15,699, 11,961, 2672, 7278 contigs (≥ 200 nt) for untreated control adult females, untreated control adult males, permethrin-treated surviving adult males and permethrin + piperonyl butoxide-treated killed adult males, respectively. More than 56% of the assembled contigs of each data set had significant hits in the BlastX (UniProtKB/Swiss-Prot database) (E <0.001). The number of contigs in each data set with InterProScan, GO mapping, Enzyme codes and KEGG pathway annotations were: Untreated Control Adult Females – 10,331, 8770, 2963, 2183; Untreated control adult males – 8392, 7056, 2449, 1765; Permethrin-treated surviving adult males – 1992, 1609, 641, 495; Permethrin + PBO-treated killed adult males – 5561, 4463, 1628, 1211.,Data is with this article and also available at the National Center for Biotechnology Information (NCBI) Short Read Archive (SRA) through the direct link https://www.ncbi.nlm.nih.gov/sra/SRP131897 or through SRA accession number SRP131897. The adult horn fly transcriptome Shotgun Assembly project has been deposited at DDBJ/EMBL/GenBank under the accession GGLM00000000. The version described in this paper is the first version, GGLM01000000. The overall BioProject ID is PRJNA429442 and the BioSample accessions are SAMN08355023, SAMN08355024, SAMN08355025, and SAMN08355026.,,